Regulation of RNA polymerase II (Pol II) transcription within a genome is essential for cell survival and differentiation. One protein complex involved in this regulation in eukaryotes is the Paf1 complex (Paf1C), which is best studied for promoting transcription elongation and histone modifications. A less well understood function of the Paf1C is its contribution to termination of noncoding RNA (ncRNA) transcripts, which have a myriad of important cellular functions. Like Paf1C, ncRNAs have been implicated in a range of human diseases including cancer. The long-term goal of this research proposal is to elucidate the underlying mechanisms via which transcription of ncRNAs is controlled in S. cerevisiae. In Specific Aims 1 and 2, the role of the Paf1C in the transcription of ncRNAs throughout the genome will be defined with high-density tiling arrays and confirmed directly with RNA analysis and the use of established genetic reporter constructs. Additionally, targeted biochemical experiments will characterize how a network of proteins, including the Paf1C subunits, work together on a molecular level to regulate ncRNA transcription and function. A genetic screen, described in Specific Aim 3, will identify novel paf1 mutations that impair ncRNA transcription termination. Characterizing these mutations will reveal whether the ncRNA functions of Paf1C overlap with the other established roles of Paf1C, such as promoting histone modifications. Overall, these experiments addressing ncRNA regulation and conserved Paf1C functions will define the molecular interplay of a network of proteins involved in central regulatory mechanisms, which in turn will shed light on how perturbations of Paf1C and ncRNAs can lead to disease progression. PUBLIC HEALTH RELEVANCE: Non-coding RNAs (ncRNAs) perform a myriad of functions important for cell growth. Experiments in this proposal will determine the molecular mechanisms and coordinated action of a network of proteins that are responsible for the regulation of ncRNA synthesis throughout the genome. Shedding light on these key cellular processes is important because perturbations of these regulatory proteins and ncRNAs can lead to human diseases such as cancer.